abbinding Class Reference

Inheritance diagram for abbinding:

Public Member Functions
	abbinding ()
virtual	~abbinding ()
void	set_default ()
void	init_options ()
void	set_file_name (utility::file::FileName pdb_file_name)
void	set_partners (std::string partner_info)
void	set_pre_process (bool pre_process)
void	set_refine (bool refine)
void	set_output_raw_scores (bool output_raw_scores)
void	set_cognate_partners (std::string cognate_partner_info)
void	set_cognate_pdb (utility::file::FileName cognate_pdb)
void	setup_foldtree (core::pose::Pose &pose, std::string partner_chainID)
utility::vector1< core::Real >	return_raw_scores (const core::pose::Pose &pose)
void	superimpose_antigen (core::pose::Pose &pose1, core::pose::Pose const &pose2, std::string const &ant1_chains, std::string const &ant2_chains)
core::Real	rmsd_frmk_chothia_num_ab (pose::Pose const &pose1, pose::Pose const &pose2, std::string const &ab1_chains, std::string const &ab2_chains)
utility::vector1< std::string >	partners_from_info (std::string const partner_info)
void	setup_task_and_repack (core::pose::Pose &pose)
utility::vector1< core::Real >	calc_energies_and_sasa (const core::pose::Pose &pose, core::scoring::ScoreFunctionOP scorefxn, utility::vector1_int movable_jumps, bool output_raw_scores)
protocols::antibody2::LHRepulsiveRampOP	setup_RepulsiveRampMover (core::pose::Pose &pose)
virtual void	apply (core::pose::Pose &pose)
std::string	get_name () const
virtual protocols::moves::MoverOP	fresh_instance () const
virtual bool	reinitialize_for_each_job () const
virtual bool	reinitialize_for_new_input () const

Private Attributes
utility::file::FileName	pdb_file_name_
std::string	partner_info_
std::string	cognate_partner_info_
utility::file::FileName	cognate_pdb_
utility::vector1_int	movable_jumps_
bool	refine_
bool	pre_process_
bool	output_raw_scores_
bool	cognate_
core::Real	frmk_rms_
utility::vector1< utility::file::FileName >	unbound_pdbs_

Constructor & Destructor Documentation

abbinding()

abbinding::abbinding ( )

inline

~abbinding()

virtual abbinding::~abbinding ( )

inlinevirtual

Member Function Documentation

apply()

virtual void abbinding::apply ( core::pose::Pose &  pose )

inlinevirtual

References pyrosetta::create_score_function, bin_torsions::job, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, beta_nonlocal::score_fxn, and basic::options::OptionKeys::frags::scoring::scoring.

Referenced by pyrosetta.distributed.tasks.rosetta_scripts.BaseRosettaScriptsTask::execute().

calc_energies_and_sasa()

utility::vector1< core::Real > abbinding::calc_energies_and_sasa ( const core::pose::Pose &  pose, core::scoring::ScoreFunctionOP  scorefxn, utility::vector1_int  movable_jumps, bool  output_raw_scores  )

inline

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, basic::options::OptionKeys::pH::output_raw_scores, beta_nonlocal::pose, oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, and basic::options::OptionKeys::enzdes::trans_magnitude.

fresh_instance()

virtual protocols::moves::MoverOP abbinding::fresh_instance ( ) const

inlinevirtual

get_name()

std::string abbinding::get_name ( ) const

inline

init_options()

void abbinding::init_options ( )

inline

References basic::options::OptionKeys::pH::cognate_partners, basic::options::OptionKeys::pH::cognate_pdb, basic::options::OptionKeys::docking::docking_local_refine, option, basic::options::OptionKeys::pH::output_raw_scores, basic::options::OptionKeys::docking::partners, basic::options::OptionKeys::pH::pre_process, docking::s, and basic::options::OptionKeys::inout::dbms::user.

partners_from_info()

utility::vector1< std::string > abbinding::partners_from_info ( std::string const  partner_info )

inline

References create_a3b_hbs::i, basic::options::OptionKeys::docking::partners, and binder::split().

reinitialize_for_each_job()

virtual bool abbinding::reinitialize_for_each_job ( ) const

inlinevirtual

reinitialize_for_new_input()

virtual bool abbinding::reinitialize_for_new_input ( ) const

inlinevirtual

return_raw_scores()

utility::vector1< core::Real > abbinding::return_raw_scores ( const core::pose::Pose &  pose )

inline

References beta_nonlocal::pose, and basic::options::OptionKeys::frags::scoring::scoring.

rmsd_frmk_chothia_num_ab()

core::Real abbinding::rmsd_frmk_chothia_num_ab ( pose::Pose const &  pose1, pose::Pose const &  pose2, std::string const &  ab1_chains, std::string const &  ab2_chains  )

inline

References create_a3b_hbs::i, create_a3b_hbs::j, kmeans_adaptive_kernel_density_bb_dependent_rotlib::m, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, natoms(), p2, test.T008_Serialization::pose1, test.T008_Serialization::pose2, and sum().

set_cognate_partners()

void abbinding::set_cognate_partners ( std::string  cognate_partner_info )

inline

set_cognate_pdb()

void abbinding::set_cognate_pdb ( utility::file::FileName  cognate_pdb )

inline

References basic::options::OptionKeys::pH::cognate_pdb.

set_default()

void abbinding::set_default ( )

inline

set_file_name()

void abbinding::set_file_name ( utility::file::FileName  pdb_file_name )

inline

set_output_raw_scores()

void abbinding::set_output_raw_scores ( bool  output_raw_scores )

inline

References basic::options::OptionKeys::pH::output_raw_scores.

set_partners()

void abbinding::set_partners ( std::string  partner_info )

inline

set_pre_process()

void abbinding::set_pre_process ( bool  pre_process )

inline

References basic::options::OptionKeys::pH::pre_process.

set_refine()

void abbinding::set_refine ( bool  refine )

inline

References kic_runner::refine.

setup_foldtree()

void abbinding::setup_foldtree ( core::pose::Pose &  pose, std::string  partner_chainID  )

inline

References chain_begin(), chain_end(), utility::io::oc::cout, loops::cutpoint, create_a3b_hbs::f, create_a3b_hbs::i, create_a3b_hbs::pdb_info, and beta_nonlocal::pose.

setup_RepulsiveRampMover()

protocols::antibody2::LHRepulsiveRampOP abbinding::setup_RepulsiveRampMover ( core::pose::Pose &  pose )

inline

References pyrosetta::create_score_function, basic::options::OptionKeys::in::file::movemap, beta_nonlocal::pose, vancomycin::task, basic::options::OptionKeys::task_operations::task_operations, test.G200_Module_Region::tf, and basic::options::OptionKeys::packing::unboundrot.

setup_task_and_repack()

void abbinding::setup_task_and_repack ( core::pose::Pose &  pose )

inline

References pyrosetta::create_score_function, create_a3b_hbs::ii, beta_nonlocal::pose, and basic::options::OptionKeys::frags::scoring::scoring.

superimpose_antigen()

void abbinding::superimpose_antigen ( core::pose::Pose &  pose1, core::pose::Pose const &  pose2, std::string const &  ant1_chains, std::string const &  ant2_chains  )

inline

References create_a3b_hbs::ii, beta_nonlocal::jj, test.T008_Serialization::pose1, test.T008_Serialization::pose2, and superimpose_pose().

Member Data Documentation

cognate_

bool abbinding::cognate_

private

cognate_partner_info_

std::string abbinding::cognate_partner_info_

private

cognate_pdb_

utility::file::FileName abbinding::cognate_pdb_

private

frmk_rms_

core::Real abbinding::frmk_rms_

private

movable_jumps_

utility::vector1_int abbinding::movable_jumps_

private

output_raw_scores_

bool abbinding::output_raw_scores_

private

partner_info_

std::string abbinding::partner_info_

private

pdb_file_name_

utility::file::FileName abbinding::pdb_file_name_

private

pre_process_

bool abbinding::pre_process_

private

refine_

bool abbinding::refine_

private

unbound_pdbs_

utility::vector1< utility::file::FileName > abbinding::unbound_pdbs_

private

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The documentation for this class was generated from the following file:

• src/apps/pilot/krishna/ab_binding.cc